[English] 日本語
Yorodumi
- PDB-5vwa: Y316F mutant of corn root ferredoxin:NADP+ reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vwa
TitleY316F mutant of corn root ferredoxin:NADP+ reductase
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression / TRANSFERASE
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / NADPH binding / photosynthesis / chloroplast / electron transport chain / electron transfer activity / nucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKean, K.M. / Carpenter, R.A. / Hall, A.R. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM119227 United States
National Science Foundation (NSF, United States)MCB-9982727 United States
CitationJournal: FEBS J. / Year: 2017
Title: High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily.
Authors: Kean, K.M. / Carpenter, R.A. / Pandini, V. / Zanetti, G. / Hall, A.R. / Faber, R. / Aliverti, A. / Karplus, P.A.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1563
Polymers35,3461
Non-polymers8102
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.081, 59.081, 186.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-245-

GLY

21A-954-

HOH

-
Components

#1: Protein Ferredoxin--NADP reductase


Mass: 35345.996 Da / Num. of mol.: 1 / Mutation: Y316F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22-24% PEG 8000, 0.1 M sodium cacodylate (pH 6-7), 0.18-0.22 M magnesium acetate, 100 mM nicotinamide

-
Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→11.54 Å / Num. obs: 33383 / % possible obs: 92.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 2142 / % possible all: 60.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LO8

3lo8


Resolution: 1.8→11.535 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1659 3314 9.97 %
Rwork0.1248 --
obs0.1289 33230 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→11.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 54 594 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092705
X-RAY DIFFRACTIONf_angle_d1.0163697
X-RAY DIFFRACTIONf_dihedral_angle_d13.91646
X-RAY DIFFRACTIONf_chiral_restr0.059380
X-RAY DIFFRACTIONf_plane_restr0.007485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.82580.1824880.1563686X-RAY DIFFRACTION54
1.8258-1.85290.2029900.138876X-RAY DIFFRACTION64
1.8529-1.88180.19441030.1424911X-RAY DIFFRACTION70
1.8818-1.91250.16591170.1302991X-RAY DIFFRACTION76
1.9125-1.94530.15191200.13211054X-RAY DIFFRACTION81
1.9453-1.98050.16981310.12811198X-RAY DIFFRACTION87
1.9805-2.01840.15231210.12871224X-RAY DIFFRACTION92
2.0184-2.05940.17341500.12591269X-RAY DIFFRACTION98
2.0594-2.10390.17031490.12081348X-RAY DIFFRACTION100
2.1039-2.15250.17531530.12751328X-RAY DIFFRACTION100
2.1525-2.2060.1761560.11891312X-RAY DIFFRACTION100
2.206-2.26520.1651520.1141341X-RAY DIFFRACTION100
2.2652-2.33130.18451400.12531329X-RAY DIFFRACTION100
2.3313-2.40590.18811480.11721316X-RAY DIFFRACTION100
2.4059-2.49110.17131460.12281350X-RAY DIFFRACTION100
2.4911-2.58970.14971300.12071376X-RAY DIFFRACTION100
2.5897-2.70620.15821540.12121348X-RAY DIFFRACTION100
2.7062-2.84680.17071380.12911354X-RAY DIFFRACTION100
2.8468-3.02220.18971520.13321347X-RAY DIFFRACTION100
3.0222-3.25070.15731560.13051358X-RAY DIFFRACTION100
3.2507-3.5690.1541530.11521357X-RAY DIFFRACTION100
3.569-4.06550.13991530.11341379X-RAY DIFFRACTION100
4.0655-5.04950.13751390.10291438X-RAY DIFFRACTION100
5.0495-11.53510.20481750.16891426X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -23.4673 Å / Origin y: 4.3829 Å / Origin z: -13.1159 Å
111213212223313233
T0.1235 Å20.0183 Å2-0.0219 Å2-0.0917 Å20.0072 Å2--0.1285 Å2
L0.3742 °20.158 °2-0.0007 °2-0.6132 °20.2007 °2--1.4653 °2
S0.0233 Å °-0.0109 Å °-0.0348 Å °0.0585 Å °-0.0048 Å °-0.0521 Å °0.1343 Å °0.1298 Å °-0.0098 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more